2XNI | pdb_00002xni

Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from amino cyclic boronates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.249 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2XNI

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Novel Macrocyclic Hcv Ns3 Protease Inhibitors Derived from Alpha-Amino Cyclic Boronates.

Li, X.Zhang, Y.Liu, Y.Ding, C.Z.Zhou, Y.Li, Q.Plattner, J.J.Baker, S.J.Zhang, S.Kazmierski, W.M.Wright, L.L.Smith, G.K.Grimes, R.M.Crosby, R.M.Creech, K.L.Carballo, L.H.Slater, M.J.Jarvest, R.L.Thommes, P.Hubbard, J.A.Convery, M.A.Nassau, P.M.Mcdowell, W.Skarzynski, T.J.Qian, X.Fan, D.Liao, L.Ni, Z.-J.Pennicott, L.E.Zou, W.Wright, J.

(2010) Bioorg Med Chem Lett 20: 5695

  • DOI: https://doi.org/10.1016/j.bmcl.2010.08.022
  • Primary Citation Related Structures: 
    2XNI

  • PubMed Abstract: 

    A novel series of P2-P4 macrocyclic HCV NS3/4A protease inhibitors with α-amino cyclic boronates as warheads at the P1 site was designed and synthesized. When compared to their linear analogs, these macrocyclic inhibitors exhibited a remarkable improvement in cell-based replicon activities, with compounds 9a and 9e reaching sub-micromolar potency in replicon assay. The SAR around α-amino cyclic boronates clearly established the influence of ring size, chirality and of the substitution pattern. Furthermore, X-ray structure of the co-crystal of inhibitor 9a and NS3 protease revealed that Ser-139 in the enzyme active site traps boron in the warhead region of 9a, thus establishing its mode of action.


  • Organizational Affiliation
    • Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, CA 94303, USA.

Macromolecule Content 

  • Total Structure Weight: 47.66 kDa 
  • Atom Count: 2,844 
  • Modeled Residue Count: 371 
  • Deposited Residue Count: 442 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NS3 PROTEASE
A, B
198Orthohepacivirus hominisMutation(s): 0 
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27958
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NS4A COFACTOR
C, D
23Orthohepacivirus hominisMutation(s): 0 
UniProt
Find proteins for C9WU77 (Hepacivirus hominis)
Explore C9WU77 
Go to UniProtKB:  C9WU77
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9WU77
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TR8

Query on TR8



Download:Ideal Coordinates CCD File
E [auth A](1-{[(10-tert-butyl-15,15-dimethyl-3,9,12-trioxo-6,7,9,10,11,12,14,15,16,17,18,19,23,23a-tetradecahydro-1H,5H-2,23:5,8-dimethano-4,13,2,8,11-benzodioxatriazacyclohenicosin-7(3H)-yl)carbonyl]amino}-3-hydroxypropyl)(trihydroxy)borate(1-)
C32 H52 B N4 O10
TWUMYENOHGWFCN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
I [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.249 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.289α = 90
b = 233.289β = 90
c = 78.067γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary